@Makro To start with the easiest question: no, if you deselect a POI, it does not disappear from your own POI list.
The options you are given—adding it as a POI and/or as a waypoint—allow you to choose whether to see both or just one of them. You can then place the created waypoint on the route line (for example, if the POI point is far away from the road) while leaving the original POI point in its original location.
After placing the POIs in your route, you can deselect your own library. Only the POIs that have been placed in your route will then be visible. This is especially useful if your own list contains more than 2,000 POIs, as there is a limitation in the navigation app: it displays a maximum of 2,000.
